This lizard occurs in a wide range of habitats, including creosote bush and sagebrush desert, pinyon-juniper woodland, and catclaw-cedar-grama grass associations in the eastern part of range and chaparral areas in the west; it occurs in both rocky areas and barren dunes (Grismer 2002, Stebbins 2003). Refuges during inactivity include rocks, burrows, and spaces beneath vegetative debris or trash.

The range of this species in the United States encompasses southern California, southern Nevada, southwestern Utah, western and southern Arizona (including the Little Colorado River Basin; Persons and Nowak, 2004), and extreme southwestern New Mexico. In Mexico the species occurs throughout Baja California (except high mountains) and in western Sonora (Grismer 2002, Stebbins 2003). Coleonyx variegatus also occurs on islands in the Gulf of California and off the western coast of Baja California. Its elevational range extends from below sea level in desert sinks to about 1,520 m (5,000 feet).

It occurs in many protected areas.